Sanyin Zhang’s research while affiliated with Chengdu University of Traditional Chinese Medicine and other places

For steady transgenic expression, lentiviral vector-mediated gene delivery is a commonly used technique. One question that needs to be explored is how external lentiviral vectors and overexpressed genes perturb cellular homeostasis, potentially altering transcriptional networks. In this study, two Human Embryonic Kidney 293T (HEK293T)-derived cell lines were established via lentiviral transduction, one overexpressing green fluorescent protein (GFP) and the other co-overexpressing GFP and ADORA3 following puromycin selection to ensure stable genomic integration. Genes with differentially transcript utilization (gDTUs) and differentially expressed genes (DEGs) across cell lines were identified after short-read and long-read RNA-seq. Only 31 genes were discovered to have changed in expression when GFP was expressed, although hundreds of genes showed variations in transcript use. In contrast, even when co-overexpression of GFP and ADORA3 alters the expression of more than 1000 genes, there are still less than 1000 gDTUs. Moreover, DEGs linked to ADORA3 overexpression play a major role in RNA splicing, whereas gDTUs are highly linked to a number of malignancies and the molecular mechanisms that underlie them. For the analysis of gene expression data from stable cell lines derived from HEK293T, our findings provide important insights into changes in gene expression and alternative splicing.

Phenotypic modifications and their effects on cellular functions through the up-regulation of target gene expression have frequently been observed in genetic studies, but the unique roles of cell lines and their introduced plasmids in influencing these functions have not been fully revealed. In this research, we developed two distinct cell lines derived from the A549 cell line: one that stably overexpresses GFP and another that is a polyclonal stable line overexpressing both GFP and P2RY12. We then utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and genes with differential transcript usage (gDTUs) after GFP overexpression (GFP-OE) and P2RY12 overexpression (P2RY12-OE). We found that, compared with A549, there were more than 1700 differentially expressed genes (DEGs) in both GFP-OE and P2RY12-OE cells, while only 866 DEGs were identified in GFP-OE and P2RY12-OE cells. Notably, the differences in transcript usage were relatively minor, with only over 400 genes exhibiting changes across all three groups. The functional analysis of DEGs and gDTUs showed that they were both highly enriched in the pathways associated with cell proliferation and migration. In summary, we performed an extensive analysis of the transcriptome profile of gene expression and alternative splicing with GFP-OE and P2RY12-OE, enhancing our comprehension of how genes function within cells and the processes that control gene expression.

Screening for pulmonary nodules (PN) using low-dose CT has proven effective in reducing lung cancer (LC) mortality. However, current treatments relying on follow-up and surgical excision fail to fully address clinical needs. Pathological angiogenesis plays a pivotal role in supplying oxygen necessary for the progression of PN to LC. The interplay between hypoxia and angiogenesis establishes a vicious cycle, rendering anti-angiogenesis therapy alone insufficient to prevent PN to LC transformation. In traditional Chinese medicine (TCM), PN is referred to as “Feiji,” which is mainly attributed to Qi and blood deficiency, correspondingly, the most commonly prescribed medicines are Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao (huang qi) (AR) and Angelica sinensis (Oliv.) Diels (dang gui) (ARS). Modern pharmacological studies have demonstrated that AR and ARS possess immune-enhancing, anti-tumor, anti-inflammatory, and anti-angiogenic properties. However, the precise mechanisms through which AR and ARS exert anti-angiogenic effects to delay PN progression to LC remain inadequately understood. This review explores the critical roles of hypoxia and angiogenesis in the transition from PN to LC. It emphasizes that, compared to therapies targeting angiogenic growth factors alone, AR, ARS, and their compound-based prescriptions offer additional benefits. These include ameliorating hypoxia by restoring blood composition, enhancing vascular structure, accelerating circulation, promoting vascular normalization, and blocking or inhibiting various pro-angiogenic expressions and receptor interactions. Collectively, these actions inhibit angiogenesis and delay the PN-to-LC transformation. Finally, this review summarizes recent advancements in related research, identifies existing limitations and gaps in knowledge, and proposes potential strategies and recommendations to address these challenges.

Traditional medicines serve not only as an integral part of medical treatments prescribed by healthcare providers but also as a fundamental reservoir for novel molecular scaffolds. However, gaps remain in our understanding of the mechanisms underlying their activity. A superfamily of membrane proteins, G protein-coupled receptors (GPCRs), have been demonstrated to be potential targets for several compounds isolated from traditional medicines. Given that GPCRs serve as targets for approximately one-third of all marketed drugs, they may be compelling targets for repurposing traditional medicines. Despite this potential, research investigating their activity or potential ligands across GPCRome, the library of human GPCRs, is scarce. Drawing on the functional and structural knowledge presently available, this review contemplates prospective trends in GPCR drug discovery, proposes innovative strategies for investigating traditional medicines, and highlights ligand screening approaches for identifying novel drug-like molecules. To discover bioactive molecules from traditional medicines that either directly bind to GPCRs or indirectly modify their function, a genome-wide pan-GPCR drug discovery platform was designed for the identification of bioactive components and targets, and the evaluation of their pharmacological profiles. This platform aims to aid the exploration of all-sided relations between traditional medicines and GPCRome using advanced high-throughput screening techniques. We present various approaches used by many, including ourselves, to illuminate the previously unexplored aspects of traditional medicines and GPCRs.

G protein-coupled receptors (GPCRs) widely exist in vivo and participate in many physiological processes, thus emerging as important targets for drug development. Approximately 30% of the Food and Drug Administration (FDA)-approved drugs target GPCRs. To date, the ‘one disease, one target, one molecule’ strategy no longer meets the demands of drug development. Meanwhile, small-molecule drugs account for 60% of FDA-approved drugs. Traditional Chinese medicine (TCM) has garnered widespread attention for its unique theoretical system and treatment methods. TCM involves multiple components, targets and pathways. Centered on GPCRs and TCM, this paper discusses the similarities and differences between TCM and GPCRs from the perspectives of syndrome of TCM, the consistency of TCM’s multi-component and multi-target approaches and the potential of GPCRs and TCM in the development of novel drugs. A novel strategy, ‘simultaneous screening of drugs and targets’, was proposed and applied to the study of GPCRs. We combine GPCRs with TCM to facilitate the modernisation of TCM, provide valuable insights into the rational application of TCM and facilitate the research and development of novel drugs. This study offers theoretical support for the modernisation of TCM and introduces novel ideas for development of safe and effective drugs.

Cepharanthine, a secondary metabolite isolated from Stephania, has garnered attention for its reported effectiveness against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). To discover more cepharanthine analogs with anti-coronavirus properties, we assembled three Stephania genomes, proposed the cepharanthine biosynthetic pathway, and assessed the antiviral potential of compounds involved in the pathway. Nearly perfect telomere-to-telomere assembly with one remaining gap has been obtained for the S. japonica genome. Genome-guided cepharanthine analogs mining in Stephania was performed to identify cepharanthine-related metabolites with anti-coronavirus properties, and seven cepharanthine analogs can broad-spectrum inhibit coronavirus including SARS-CoV-2, GX_P2V, SADS-CoV and PEDV infection. Two other genera that produce cepharanthine analogs, Nelumbo and Thalictrum, are also believed to have potential for antiviral compound discovery. Here, we have systematically assessed anti-coronavirus activity of a series of cepharanthine metabolites from the viewpoint of biosynthesis pathway, our study will provide an opportunity to accelerate broad-spectrum anti-coronavirus drug discovery.

Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 Mb and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that Mentha suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the Mentha suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, Mentha suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.